Reaction of Amino Acids,Di‐ and Tripeptides with the Environmental Oxidant NO3.: A Laser Flash Photolysis and Computational Study

Absolute rate coefficients for the reaction between the important environmental free radical oxidant NO₃^. and a series of N‐ and C‐protected amino acids, di‐ and tripeptides were determined using 355 nm laser flash photolysis of cerium(IV) ammonium nitrate in the presence of the respective substrates in acetonitrile at 298±1 K. Through combination with computational studies it was revealed that the reaction with acyclic aliphatic amino acids proceeds through hydrogen abstraction from the α‐carbon, which is associated with a rate coefficient of about 1.8×10⁶ m ^?1 s^?1 per abstractable hydrogen atom. The considerably faster reaction with phenylalanine [k=(1.1±0.1)×10⁷ m ^?1 s^?1] is indicative for a mechanism involving electron transfer. An unprecedented amplification of the rate coefficient by a factor of 7–20 was found with di‐ and tripeptides that contain more than one phenylalanine residue. This suggests a synergistic effect between two aromatic rings in close vicinity, which makes such peptide sequences highly vulnerable to oxidative damage by this major environmental pollutant.     

A general strategy for creating "inactive-conformation" abl inhibitors

Kinase inhibitors that bind to the ATP cleft can be broadly classified into two groups: those that bind exclusively to the ATP site with the kinase assuming a conformation otherwise conducive to phosphotransfer (type I), and those that exploit a hydrophobic site immediately adjacent to the ATP pocket made accessible by a conformational rearrangement of the activation loop (type II). To date, all type II inhibitors were discovered by using structure-activity-guided optimization strategies. Here, we describe a general pharmacophore model of type II inhibition that enables a rational "hybrid-design" approach whereby a 3-trifluoromethylbenzamide functionality is appended to four distinct type I scaffolds in order to convert them into their corresponding type II counterparts. We demonstrate that the designed compounds function as type II inhibitors by using biochemical and cellular kinase assays and by cocrystallography with Abl.     

Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulators with Forecaster, a novel platform for drug discovery

As part of a large medicinal chemistry program, we wish to develop novel selective estrogen receptor modulators (SERMs) as potential breast cancer treatments using a combination of experimental and computational approaches. However, one of the remaining difficulties nowadays is to fully integrate computational (i.e., virtual, theoretical) and medicinal (i.e., experimental, intuitive) chemistry to take advantage of the full potential of both. For this purpose, we have developed a Web-based platform, Forecaster, and a number of programs (e.g., Prepare, React, Select) with the aim of combining computational chemistry and medicinal chemistry expertise to facilitate drug discovery and development and more specifically to integrate synthesis into computer-aided drug design. In our quest for potent SERMs, this platform was used to build virtual combinatorial libraries, filter and extract a highly diverse library from the NCI database, and dock them to the estrogen receptor (ER), with all of these steps being fully automated by computational chemists for use by medicinal chemists. As a result, virtual screening of a diverse library seeded with active compounds followed by a search for analogs yielded an enrichment factor of 129, with 98% of the seeded active compounds recovered, while the screening of a designed virtual combinatorial library including known actives yielded an area under the receiver operating characteristic (AU-ROC) of 0.78. The lead optimization proved less successful, further demonstrating the challenge to simulate structure activity relationship studies.     

Conditions to Control Furan Ring Opening during Furfuryl Alcohol Polymerization

The chemistry of biomass-derived furans is particularly sensitive to ring openings. These side reactions occur during furfuryl alcohol polymerization. In this work, the furan ring-opening was controlled by changing polymerization conditions, such as varying the type of acidic initiator or the water content. The degree of open structures (DOS) was determined by quantifying the formed carbonyl species by means of quantitative ¹⁹F NMR and potentiometric titration. The progress of polymerization and ring opening were monitored by DSC and FT-IR spectroscopy. The presence of additional water is more determining on ring opening than the nature of the acidic initiator. Qualitative structural assessment by means of ¹³C NMR and FT-IR shows that, depending on the employed conditions, poly(furfuryl alcohol) samples can be classified in two groups. Indeed, either more ester or more ketone side groups are formed as a result of side ring opening reactions. The absence of additional water during FA polymerization preferentially leads to opened structures in the PFA bearing more ester moieties.     

Small molecules that induce cardiomyogenesis in embryonic stem cells

A phenotypic cell-based screen of a large combinatorial chemical library led to the identification of a class of diaminopyrimidine compounds (cardiogenol A-D) which can selectively and efficiently induce mouse embryonic stem cells (ESCs) to differentiate into cardiomyocytes. ESC-derived cardiomyocytes were shown to express multiple cardiac muscle markers, including myosin heavy chain, GATA-4, MEF2, and Nkx2.5, and spontaneously form beating regions. Such small molecules will serve as useful chemical probes to study cardiac muscle differentiation and may ultimately facilitate the therapeutic application of ESCs for cardiac repair.     

High-performance liquid chromatography of deferoxamine and ferrioxamine: interference by iron present in the chromatographic system

The assay of the complexed (ferrioxamine) and uncomplexed forms of deferoxamine, a strong iron(III) chelating agent, by reversed-phase high-performance liquid chromatography was investigated. Complex formation with trace amounts of iron in the chromatographic system hinders the assay of deferoxamine by causing appearance of unexpected peaks, reaction zones and variations in retention time. By purging the column with deferoxamine and using EDTA in the mobile phase, these adverse effects in the determination of deferoxamine were eliminated. No interference by iron contamination of the chromatographic system was found in the assay of ferrioxamine, which is facilitated by the strong absorption of the analyte at 430 nm.     

Identification of a novel protein regulating microtubule stability through a chemical approach

To identify novel proteins regulating the microtubule cytoskeleton, we screened a library of purine derivatives using mitotic spindle assembly in Xenopus egg extracts as an assay. Out of a collection of 1561 compounds, we identified 15 that destabilized microtubules without targeting tubulin directly, resulting in small spindles. Affinity chromatography with one compound, named diminutol, revealed a potential target as NQO1, an NADP-dependent oxidoreductase. A role for NQO1 in influencing microtubule polymerization was confirmed through inhibition studies using known inhibitors and immunodepletion. Therefore, this chemical approach has identified a novel factor required for microtubule morphogenesis and cell division.     

Time-resolved light scattering studies of Spin-coated titanium dioxide

Spin coating of titanium alkoxides is a fast and straightforward method of forming compact and durable titanium dioxide thin films. In this report, an optical interference technique is used to understand the dynamics of titanium dioxide thin film formation during the spin coating process of titanium (IV) ethoxide sols, and a 4-stage thinning model is proposed. Optical monitoring of interference fringes as a function of time enables determination of the time-dependent film thickness through measurement of the interference fringe separation while the sol to gel transition can be monitored by analyzing the fringe visibility. For films that are spun at 2,000 rpm or faster, a spin duration of 5 s is sufficient for the film to reach its final thickness. At a given spin speed, spin times longer than 5 s do not affect the final film thickness. However, thinner final film thicknesses can be achieved by increasing the spin speed. All films were found to densify on annealing with an annealed thickness approximately 0.4 times that of the pre-anneal thickness regardless of spin speed. Spin-coated titanium dioxide films are expected to play an important role in low-cost and scalable next generation solar cells employing dyes and quantum dots as the light harvesting agents.